Name: Rhodovulum imhoffii JA125
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13748

Type strain:

Species: Rhodovulum imhoffii

Strain Designation: JA125

Culture col. no.: DSM 18064, CIP 109541, JCM 13589

Strain history: Ch. Sasikala JA125.

NCBI tax ID(s): 365340 (species)

SI-ID 297330

DSM 18064, JCM 13589

Section

Rhodovulum imhoffii JA125 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from marine aquaculture pond.

Gram-negative
rod-shaped
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Rhodovulum*
	Species	**Rhodovulum imhoffii**
	Full Scientific Name (LPSN)	Rhodovulum imhoffii Srinivas et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31834]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #31834]	Cell length	1 µm

[Ref.: #31834]	Cell width	0.5 µm

[Ref.: #31834]	Cell shape	rod-shaped

[Ref.: #31834]	Motility	no

[Ref.: #31834]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31834]	growth	20-35 °C
[Ref.: #31834]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #31834]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31834]			optimum	7.5
[Ref.: #31834]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7357]	Oxygen tolerance	anaerobe
[Ref.: #31834]	Oxygen tolerance	facultative anaerobe

[Ref.: #31834]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.953

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31834]		NaCl		growth	0.5-7	%
[Ref.: #31834]		NaCl		optimum	2.25	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31834]	acetate ChEBI	+	carbon source
[Ref.: #31834]	aspartate ChEBI	+	carbon source
[Ref.: #31834]	glutamate ChEBI	+	carbon source
[Ref.: #31834]	glycerol ChEBI	+	carbon source
[Ref.: #31834]	malate ChEBI	+	carbon source
[Ref.: #31834]	pyruvate ChEBI	+	carbon source
[Ref.: #31834]	succinate ChEBI	+	carbon source
[Ref.: #31834]	urea ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31834]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	chlorophyll metabolism	50	9 of 18
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7357]	Sample type/isolated from	marine aquaculture pond
[Ref.: #7357]	Geographic location (country and/or sea, region)	Bhimunipatnam
[Ref.: #7357]	Country	India
[Ref.: #7357]	Country ISO 3 Code	IND
[Ref.: #7357]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Marine aquaculture pond
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Aquaculture
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Pond (small)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM180953 (>99% sequence identity) for Rhodovulum imhoffii subclade from Microbeatlas

Aquatic Samples	261
Soil Samples	79
Animal Samples	55
Plant Samples	23
Total Samples	418

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7357]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7357]	Rhodovulum imhoffii 16S rRNA gene, type strain JA125	AM180953	1398	ENA	365340 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodovulum imhoffii DSM 18064	GCA_003046545	scaffold	GenBank	365340 tax ID	*
[Ref.: #66792]	Rhodovulum imhoffii DSM 18064	GCA_016653305	scaffold	GenBank	365340 tax ID	*
[Ref.: #66792]	Rhodovulum imhoffii strain DSM 18064	365340.5	wgs	PATRIC	365340 tax ID	*
[Ref.: #66792]	Rhodovulum imhoffii strain DSM 18064	365340.4	wgs	PATRIC	365340 tax ID	*
[Ref.: #66792]	Rhodovulum imhoffii DSM 18064	2734482186	draft	JGI IMG/M	365340 tax ID	*

[Ref.: #7357]	GC-content	58 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31834]	GC-content	58 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodovulum imhoffii DSM 18064 NCBI: GCA_003046545.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodovulum imhoffii DSM 18064 NCBI: GCA_003046545.1
[Ref.: #69480]	flagellated	no	76.533	no
[Ref.: #69480]	gram-positive	no	99.093	no
[Ref.: #69480]	anaerobic	no	65.613	no
[Ref.: #69480]	halophile	yes	67.402	no
[Ref.: #69480]	spore-forming	no	95.643	yes
[Ref.: #69480]	thermophile	no	64.366	yes
[Ref.: #69480]	glucose-util	yes	62.982	no
[Ref.: #69480]	aerobic	no	85.111	yes
[Ref.: #69480]	motile	yes	51.346	yes
[Ref.: #69480]	glucose-ferment	no	88.752	no

Availability in culture collections External links

[Ref.: #7357]

Culture collection no.

DSM 18064, CIP 109541, JCM 13589

[Ref.: #82930]

SI-ID 297330

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodovulum imhoffii sp. nov.	Srinivas TNR, Kumar PA, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.64470-0	2007	*

References

#7357

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18064

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#31834

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28100 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82930

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297330.1 )

#28100

IJSEM 228 2007 ( DOI 10.1099/ijs.0.64470-0 , PubMed 17267955 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rhodovulum imhoffii in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Rhodovulum imhoffii DSM 18064

Rhodovulum imhoffii DSM 18064

Change proposal

Change proposal